Physics-driven discovery of novel small therapeutic compounds for use as a bcl-2 inhibitor

ABSTRACT

The invention relates to compound shown with formula (I) or a pharmaceutically acceptable derivative thereof for use as a novel inhibitor of BCL-2.

TECHNICAL BACKGROUND

Finding a cure for cancer is still a demanding mission in spite of thefact that molecular mechanisms and causal relationships participating inthe, pathology of cancer have been comprehended since the mid-1980s.Programmed cell death, also known as apoptosis, is a molecular pathwaythat results with self-destruction of the cell either followingtermination of physiological function, or after a crucial damage togenetic material. The well-defined basic apoptosis pathways, extrinsicand the intrinsic pathways are variously stimulated, and they usedetermined signaling elements. The extrinsic pathway is activated byouter stimulation of death receptors. Death receptors are members of thetumor necrosis factor (TNF) receptor family which has an intracellulardeath domain that is able to accumulate and trigger caspase-8 followedby operation of effector caspases including caspase-3, -6 or -7.

This accumulation is not accompanied by direct participation of B-cellleukemia/lymphoma-2 (BCL-2). The intrinsic pathway also calledmitochondrial pathway is initiated by a variety of cytotoxic damages orgrowth signals, some of which are genetic instability, inadequatedevelopmental stimulation, invasion by viral pathogens. BCL-2 tightlyregulates this process and subsequently leads to the activation ofcaspase-9 (Cory et al., 2003; Eimon et al., 2010; Youle et al., 2008).

All members of BCL-2 protein family have retained sequence patternsregarded as the BCL-2 homology (BH) domains and could be divided into 3main classes. The first class of proteins are made up of thepro-apoptotic activator BH domain 3 (BH3) only proteins such as BIM,BID, PUMA. Immediately upon their activation, they serve as molecularguardians that connect outer spurs to the mitochondrial pathway. Thefollowing group contains the proapoptotic effectors which aremultidomain proteins, such as BAX, BAK and each of them has three BHdomains. These proteins distort the integrity of mitochondrial outermembrane, which leads to free movement of cytochrome C to cytoplasm,initiates downstream caspase activity, and ultimately to the terminationof cell, as soon as triggered. The last class of BCL-2 family are theantiapoptotic protein, BCL-XL, BCL-2, MCL-1, etc. All of these membersconsist of four BH domains and keeps cells safe by segregating theirproapoptotic peers. The most important point in promoting apoptosis isto increase the amount of BH3-only proteins or switch off one of itsantiapoptotic BCL-2 counterparts.

Apoptotic cell death is an innate hurdle to growth of tumor cells, henceone of the key hallmarks of cancer cells is the avoidance of apoptosiswhich comprises a crucial process in resistance to chemotherapeutics.This phenomenon led peculiar approaches in anticancer therapies focusingon apoptosis including suppression of survival factors that are detectedto be overexpressed in numerous malignancies.

STATE OF THE ART

The idea of BH3 mimetics as promising anticancer drugs inspired by theconclusion that a great deal of cancers rely on BCL-2 family proteinsand that the interaction between these proteins occur through specificBH domains. A genuine BH3 mimetic is expected to imitate the BH3 domainof a proapoptotic BCL-2 protein, thus deactivating the antiapoptoticfamily members by filling up their BH3-binding pockets.

Inhibition of anti-apoptotic protein BCL-2 that is overexpressed incancer cells is one of the most studied approaches in cancer research.Currently, venetoclax is the only approved drug by Food and DrugAdministration (FDA) for the treatment chronic lymphocytic leukemia(CLL) and it is a selective BCL-2 protein inhibitor. Although it has avery high affinity for BCL-2 as shown in various studies performed ondifferent cancer cell lines, resistance to this drug have already beenobserved. Hence, it is necessary to suggest new compounds and scaffoldsas BCL-2 inhibitors that could be more efficient against mutations onthe target structure and have no side effects.

The inventors have found that a new compound shown with Formula I actsas an inhibitor of BCL-2.

The compound shown with formula I according to present invention is thusa representative of a novel compound that is suitable for use in severaldisorders where an inhibition of BCL-2 protein produces atherapeutically desirable result. Such diseases can for example beproliferative diseases such as cancer. Therefore, present invention notonly relates to novel compounds shown with formula I but also to use ofsaid compounds for treatment of proliferative diseases such as cancer.

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to compound shown with formula I, which isDRG-BCL2-2, or a pharmaceutically acceptable derivative thereof.

Unless specified otherwise, the terms “compound of the presentinvention” or “compound of invention” or “compound of formula I” or“compound shown with formula I” are used interchangeable and refer tocompounds of formula I and salts thereof, hydrates or solvates of thecompound of formula I or its salts, all possible stereoisomers(diastereomers and enantiomers), tautomers, isotopically labeledcompounds (including deuterium substitutions), or its forms that formunder physiological conditions of the human body, as well as inherentlyformed moieties (e.g., polymorphs, solvates and/or hydrates).

In other words, the term “pharmaceutically acceptable derivativethereof” refers to hydrates, solvates, prodrugs, all possiblestereoisomers, salts, esters, tautomers, isotopically labeledderivatives or forms of compound of formula I that form underphysiological conditions of the human body.

Several embodiments of the invention are described herein. It must beconsidered that each specified embodiment can be combined with otherspecified features to provide further embodiments. The terms used in thesingular will also include plural and vice versa.

As disclosed herein the term “enantiomers” mean a pair of stereoisomersthat are non-superimposable mirror images of each other. A 1:1 mixtureof a pair of enantiomers is a “racemic” mixture. The absolutestereochemistry is specified according to the Cahn-Ingold-Prelog R-Ssystem. When a compound is a pure enantiomer the stereochemistry at eachchiral carbon may be specified by either R or S. Compound of formula Ihas a chiral center. In a preferred embodiment of the invention compoundof formula I is in the form of a 1:1 racemic mixture of R and Senantiomers. The compound of formula I can also be in pure R form or inpure S form or a mixture thereof in any ratio.

The present invention includes all possible isomers including racematesand optically pure forms of compound of formula I. Said forms can beprepared by using conventional techniques known in the art such as byuse of chiral reagents or other methods.

As disclosed herein the term “salts” mean acid addition of base additionsalts of the compound of invention. In particular the salts include “thepharmaceutically acceptable salts” which refer to salts that retain thebiological effectiveness and effectiveness of the compound of inventionwhile not having any biologically or otherwise unwanted properties suchas toxicity or causing any kind of formulation difficulties.

Pharmaceutically acceptable acid addition salts can be formed withorganic acids and/or inorganic acids. Acid addition salts of thecompound according to present invention can be selected from a groupcomprising; acetate, aspartate, benzoate, besylate,bromide/hydrobromide, bicarbonate/carbonate, bisulfate/sulfate,camphorsulfonate, chloride/hydrochloride, chlortheophyllonate, citrate,ethandisulfonate, fumarate, gluceptate, gluconate, glucuronate,hippurate, hydroiodide/iodide, isethionate, lactate, lactobionate,lauryl sulfate, malate, maleate, malonate, mandelate, mesylate,methylsulphate, naphthoate, napsylate, nicotinate, nitrate,octadecanoate, oleate, oxalate, palmitate, pamoate, phosphate/hydrogenphosphate/dihydrogen phosphate, polygalacturonate, propionate, stearate,succinate, sulfosalicylate, tartrate, tosylate and trifluoroacetatesalts.

Pharmaceutically acceptable base addition salts can be formed withorganic bases and/or inorganic bases. Bases appropriate for preparationof base addition salts of the compound of the invention can be selectedfrom sodium hydroxide, sodium carbonate, sodium bicarbonate, calciumhydroxide, calcium carbonate, calcium bicarbonate, magnesium hydroxide,magnesium carbonate, magnesium bicarbonate, potassium hydroxide,potassium carbonate, potassium bicarbonate and the like.

As disclosed herein the term “isotopically labeled compounds” refers tocompounds of formula I wherein one or more atoms are replaced with anatom having selected atomic mass or mass number. Such replacements canbe made with for example; ²H, ³H, ¹¹C, ¹³C, ¹⁴C, ¹⁵N, ¹⁸F ³¹P, ³²P, ³⁵S,³⁶Cl, ¹²⁵I. Such isotopically labeled variants of compound of theinvention can be used for detection or imaging techniques known in theart or for radioactive treatment of patients.

In another aspect present invention relates to pharmaceuticalcompositions comprising compound of formula I, DRG-BCL2-2, or apharmaceutically acceptable derivative thereof and at least onepharmaceutically acceptable excipient.

In a preferred embodiment of the invention, the pharmaceuticallyacceptable excipient can be selected from a group comprising; solvents,antioxidants, preservatives (e.g. antibacterial agents, antifungalagents), isotonic agents, absorption delaying agents, salts,preservatives, stabilizers, binders, disintegrants, lubricants,sweetening agents, flavoring agents and combinations thereof. Particularexamples of each group are disclosed in Remington's PharmaceuticalSciences, 18th Ed. Mack Printing Company, 1990 and incorporated hereinby reference.

The pharmaceutical compositions comprising compound of formula I or apharmaceutically acceptable derivative thereof can be formulated fordifferent routes of administration. In an embodiment of the invention,pharmaceutical compositions comprising compound of formula I can beformulated for oral administration, parenteral administration, topicaladministration or rectal administration.

In a preferred embodiment of the invention, pharmaceutical compositionsof the invention for oral administration can be in the form of tablets,lozenges, aqueous or oily suspensions, dispersible powders or granules,emulsion, hard or soft capsules, or syrups or elixirs.

In a preferred embodiment of the invention, pharmaceutical compositionsof the invention for parenteral administration can be in the form ofisotonic solutions or suspensions or in to form of lyophilized powdersuitable for reconstitution prior to administration. Said pharmaceuticalcompositions of the invention for parenteral administration can be forintramuscular, intravenous, subcutaneous, intraperitoneal, intratrachealadministration.

In a preferred embodiment of the invention, pharmaceutical compositionsof the invention for topical administration can be in the form ofaqueous solutions, suspensions, ointments, pastes, lotions, transdermalpatches, gels, creams, or sprayable formulations such as aerosols. Suchtopical administration covers administration through skin, eye or nose(i.e. intranasal administration). Thus, pharmaceutical compositions ofthe invention can be in the form of dry powders, solutions or aerosolsfor administration through pressurized containers, pump, spray, atomizeror nebulizer with or without a suitable propellant.

The pharmaceutical composition or combination of the present inventioncan be in unit dosage of about 1-1000 mg of active ingredient(s) for asubject of about 50-70 kg, or about 1-500 mg or about 1-250 mg or about1-150 mg or about 0.5-100 mg, or about 1-50 mg of active ingredients.The therapeutically effective dosage of a compound, the pharmaceuticalcomposition, or the combinations thereof, is dependent on the species ofthe subject, the body weight, age and individual condition, the disorderor disease or the severity thereof being treated. A physician, clinicianor veterinarian of ordinary skill can readily determine the effectiveamount of each of the active ingredients necessary to prevent, treat orinhibit the progress of the disorder or disease.

In a preferred embodiment, the invention, relates to compound of formulaI, DRG-BCL2-2, or a pharmaceutically acceptable derivative thereof foruse in treatment of a disorder mediated by the activity (includingnormal activity or especially over activity) of BCL2.

In an embodiment, the invention relates to compound of formula or apharmaceutically acceptable derivative thereof for use in treatment of adisorder wherein a desirable therapeutic response is observed uponadministration of a BH3 mimetic.

Within the context of this application the terms “BCL-2 inhibitor” and“BH3 mimetic” refer to the same compounds and can be usedinterchangeably.

In a preferred embodiment, a disorder mediated by the activity of BCL2is a proliferative disease such as cancer.

In an embodiment of the invention, cancer includes benign or malignanttumors, a soft tissue sarcoma or a sarcoma (e.g. liposarcoma,rhabdomyosarcoma) or bone cancer (e.g. osteosarcomas), a carcinoma (e.g.such as of the brain, kidney, liver, adrenal gland, bladder, breast,gastric, ovary, colon, rectum, prostate, pancreas, lung, vagina orthyroid), a glioblastoma, meningioma, glioma, mesothelioma, a multiplemyeloma, a gastrointestinal cancer (especially colon carcinoma orcolorectal adenoma), a tumor of the head and neck, a melanoma, aprostate hyperplasia, a neoplasia, a neoplasia of epithelial character,a leukemia such as acute myeloid leukemia or B-cell chronic lymphocyticleukemia, a lymphoma (such as of B- or T-cell origin) and metastases inother organs.

In another aspect the invention relates to the use of a compound offormula I or a pharmaceutically acceptable derivative thereof as definedherein, for the manufacture of a medicament for the treatment of adisorder or a disease in a subject mediated by the activity of BCL2.

In another aspect, the invention relates to combinations comprisingcompound of formula I or pharmaceutically acceptable derivatives thereofand one or more additional active agent selected from a groupcomprising; anti-proliferative agents, immunomodulatory agents,antiviral agents, antimicrobial agents, anti-infective agents,anti-inflammatory agents, anesthetic agents, antiemetics or combinationsthereof where appropriate. In a preferred embodiment additional activeagent is one or more anti-proliferative agent.

In an embodiment of the invention, anti-proliferative active agent canbe one or more of the agents selected from the group comprising but notlimited to; alkylating agents, anthracyclines, taxanes (cytoskeletaldisruptors), epothilones, histone deacetylase inhibitors, inhibitors oftopoisomerase I, inhibitors of topoisomerase II, kinase inhibitors,tyrosine kinase inhibitors, nucleotide analogs and precursor analogs,peptide antibiotics, platinum based agents, retinoids, vinca alkaloidsand derivatives or other agents.

Alkylating agents can be selected from a group comprising but notlimited to; bendamustine, cyclophosphamide, mechlorethamine,chlorambucil, melphalan, dacarbazine, nitrosoureas, streptozotocin,temozolomide, trabectedin.

Anthracyclines can be selected from a group comprising but not limitedto; daunorubicin, doxorubicin, epirubicin, idarubicin, mitoxantrone,valrubicin.

Taxanes (cytoskeletal disruptors) can be selected from a groupcomprising but not limited to; paclitaxel, docetaxel, abraxane,cabazitaxel,

Epothilones can be selected from a group comprising but not limited to;epothilone A, epothilone B, epothilone C, epothilone D, epothilone E,epothilone F or pharmaceutically acceptable derivatives thereof such asixabepilone.

Histone deacetylase inhibitors can be selected from a group comprisingbut not limited to; belinostat, panobinostat, valproate, vorinostat,romidepsin.

Inhibitors of topoisomerase I can be selected from a group comprisingbut not limited to; irinotecan, topotecan.

Inhibitors of topoisomerase II can be selected from a group comprisingbut not limited to; etoposide, teniposide, tafluposide.

Kinase inhibitors can be selected from a group comprising but notlimited to; bortezomib, erlotinib, gefitinib, imatinib, vemurafenib,vismodegib.

Tyrosine kinase inhibitors can be selected from a group comprising, butnot limited to, afatinib, axitinib, bosutinib, cobimetinib, crizotinib,dasatinib, erlotinib, gefitinib, imatinib, lapatinib, nilotinib,osimertinib, pazopanib, ruxolitinib, sunitinib, vandetanib.

Nucleotide analogs and precursor analogs can be selected from a groupcomprising but not limited to; azacitidine, azathioprine, cladribine,clofarabine, capecitabine, cytarabine, doxifluridine, decitabine,floxuridine, fludarabine, fluorouracil (5-FU), fluorouracil,gemcitabine, hydroxyurea, mercaptopurine, methotrexate, nelarabine,pentostatin, tioguanine, trifluridine, tipiracil.

Peptide antibiotics can be selected from a group comprising but notlimited to; bleomycin, actinomycin.

Platinum based agents can be selected from a group comprising but notlimited to; carboplatin, cisplatin, oxaliplatin.

Retinoids can be selected from a group comprising but not limited to;tretinoin, alitretinoin, bexarotene, isotretinoin, tamibarotene.

Vinca alkaloids and derivatives can be selected from a group comprisingbut not limited to; vinblastine, vincristine, vindesine, vinflunine,vinorelbine.

Other agents can be selected from a group comprising but not limited to;methotrexate, pemetrexed, pralatrexate, raltitrexed, etoposideteniposide, abiraterone, bicalutamide, cyproterone, degarelix,exemestane, fulvestrant, goserelin, histrelin, leuprolide, mifepristone,triptorelin, lenalidomide, pomalidomide, thalidomide, everolimus,temsirolimus, anagrelide, ceritinib, dabrafenib, idelalisib, ibrutinib,palbociclib, vemurafenib, bleomycin, dactinomycin, eribulin,estramustine, ixabepilone, mitomycin, procarbazine, alectinib,fluoxymesterone, iobenguane, imiquimod, interferon, ixazomib,lanreotide, lentinan, octreotide, omacetaxine, tegafur, gimeracil,oteracil, uracil, combretastatin.

In an embodiment of the invention, such combinations can be in a formwherein compound of formula I or a pharmaceutically acceptablederivative thereof and one or more therapeutically active agents,preferably anti-proliferative agents are formulated together.

In another embodiment of the invention, compound of formula I or apharmaceutically acceptable derivative thereof and one or moretherapeutically active agents, preferably anti-proliferative agents areformulated separately but they are administered to a patient in needthereof simultaneously or sequentially.

Comprising in the context of the present specification is intended tomeaning including.

Where technically appropriate, embodiments of the invention may becombined.

Embodiments are described herein as comprising certainfeatures/elements. The disclosure also extends to separate embodimentsconsisting or consisting essentially of said features/elements.

Technical references such as patents and applications are incorporatedherein by reference.

Any embodiments specifically and explicitly recited herein may form thebasis of a disclaimer either alone or in combination with one or morefurther embodiments.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

The invention will now be described with reference to the followingexamples, which are merely illustrative and should not in any way beconstrued as limiting the scope of the present invention.

EXAMPLES Example 1: Cell Culture Experiments

For cell culture experiments various cancer cell lines, HCT-116 coloncancer, U87-MG glial tumor, MCF7 breast cancer cell lines were used.Cells were seeded with high glucose DMEM medium (Biosera) supplementedwith 10% FBS (Gibco) and 1X penicillin/streptomycin (Multicell).Twenty-four hours prior to molecule treatment, 10,000 cells were seededinto each well of 24-well cell culture plates. Molecules were used bypreparing 4 mM stock solution in DMSO (Amresco). For molecule treatment,molecule stock solutions were diluted in DMEM with 10% FBS and addedonto cells in each corresponding well. Final concentration of vehicleDMSO was 2% at maximum. Therefore, the vehicle group in experiments onlyincluded maximum of 2% DMSO concentration. We calculated the number ofcells to be seeded to make sure that none of the cells reaches more than60% confluency during the treatment period, as higher plate confluencylevels would slow down cell proliferation independently from themolecule treatment.

Values of half-maximal inhibitory concentration were (IC50) determinedby MTT cell proliferation assays. Different concentrations of moleculesranging between 10-9 to 10-4 M were tested on HCT-116 cell lines withsingle treatment. 570 nm absorbance values were recorded and IC50 valueswere calculated by dose response—inhibition curves and nonlinearregression analysis on GraphPad Prism 8 software. For cell proliferationassays we performed five days experiments and repeated experiments atleast three times with all cell lines. Survival rates did not changesignificantly after third day of treatment. Therefore, three daysresults were presented. MTT analysis were performed on 24-well plateswith initially 1×104 cells/well, grown overnight, and then treated withthe selected molecules with different concentrations for at least 3days. Following the initial incubation day, molecules were added andafter incubation with MTT at 37° C. for 4 hours, formazan wassolubilized with DMSO (Sigma-Aldrich, St. Louis, USA) and absorbance wasmeasured at 570 nm. As shown by the graph in FIG. 1 , while the vehiclegroup show neat proliferation of the HCT-116 cells, the group treatedwith compound of formula I has shown reduced proliferation and apoptoticcell structures. The IC50 value of compound of formula I was determinedto be 25 μm (FIG. 1 ).

1. A compound shown with formula I which is DRG-BCL2-2, or apharmaceutically acceptable derivative thereof.


2. A compound according to claim 1 wherein pharmaceutically acceptablederivative of formula I can be its hydrates, solvates, prodrugs, allstereoisomers, salts, esters, tautomers, isotopically labeledderivatives or forms of compound of formula I that form underphysiological conditions of the human body.
 3. A compound according toclaims 1-2 for use in treatment of a disorder mediated by the activity(including normal activity or especially over activity) of BCL2.
 4. Acompound for use as claimed in claim 3 wherein the disorder is aproliferative disease.
 5. A compound for use as claimed in claim 4wherein proliferative disease is cancer.
 6. A compound for use asclaimed in claim 5 wherein cancer is benign or malignant tumors, a softtissue sarcoma or a sarcoma (e.g. liposarcoma, rhabdomyosarcoma) or bonecancer (e.g. osteosarcomas), a carcinoma (e.g. such as of the brain,kidney, liver, adrenal gland, bladder, breast, gastric, ovary, colon,rectum, prostate, pancreas, lung, vagina or thyroid), a glioblastoma,meningioma, glioma, mesothelioma, a multiple myeloma, a gastrointestinalcancer (especially colon carcinoma or colorectal adenoma), a tumor ofthe head and neck, a melanoma, a prostate hyperplasia, a neoplasia, aneoplasia of epithelial character, a leukemia such as acute myeloidleukemia or B-cell chronic lymphocytic leukemia, a lymphoma (such as ofB- or T-cell origin) and metastases in other organs
 7. A compoundaccording to claims 1-2 for use in combination with one or moreadditional pharmaceutically active agents.
 8. A compound for use asclaimed in claim 7 wherein additional pharmaceutically active agent isselected from a group comprising anti-proliferative agents,immunomodulatory agents, antiviral agents, antimicrobial agents,anti-infective agents, anesthetic agents, antiemetics or combinationsthereof.
 9. A compound for use as claimed in claim 8 whereinantiproliferative agents are selected from a group comprising alkylatingagents, anthracyclines, taxanes (cytoskeletal disruptors), epothilones,histone deacetylase inhibitors, inhibitors of topoisomerase I,inhibitors of topoisomerase II, kinase inhibitors, tyrosine kinaseinhibitors, nucleotide analogs and precursor analogs, peptideantibiotics, platinum based agents, retinoids, vinca alkaloids andderivatives or other agents.
 10. A pharmaceutical composition comprisinga compound according to claims 1-2 and at least one pharmaceuticallyacceptable excipient.
 11. A pharmaceutical composition comprising acompound according to claims 1-2 and one or more additionalpharmaceutically active agent selected from a group comprisinganti-proliferative agents, immunomodulatory agents, antiviral agents,antimicrobial agents, anti-infective agents, anesthetic agents,antiemetics or combinations thereof.